AMPDB Tutorial

1. Use AMPDB Quick Search Facility
This is also a generelized search facility like text search. This search facility is case insensitive. A user can search any search term (shown in example of SelBioDB Text Search). No search restriction is allowed here.
2. Use AMPDB Text Search Facility
This is a generelized search facility (the search can also be restricted by clicking on 'Choose a Dataset' option). This search facility is case insensitive. Here one can search with followings.
1. AMPDB ID (e.g., AMPDB_101)
2. AMP from a Organism (e.g., Papio anubis)
3. AMP name (e.g., Defensin)
4. Gene name of any AMP (e.g., LBP)
5. AMP Sequence (e.g., 'MKLSTSLLAIVAVA')
Note: This is not BLAST search
6. Existence level of a protein (e.g., Inferred from homology)
7. Target-organism (e.g., E.coli)
Note: For more specific target-organism search "Search by Target Organism" search facility is recomended.
8. Antimicrobial activity of an AMP (e.g., Fungicide)
9. Enzymatic activity of an AMP (e.g., Protease)
10. Inhibitory activity of an AMP (e.g., Protease inhibitor)
11. Other biological activity (e.g., Cytokine)
Note: For perform more specific 8 to 11 related search "Search by Activity" search facility is recomended.
12. PubMed ID (e.g., 25342741)
13. PDB ID (e.g., 2MN5)
14. IntAct ID (e.g., O16829)
15. STRING ID (e.g., 9606.ENSP00000249330)
16. MINT ID (e.g., O60814)
17. DIP ID (e.g., DIP-26293N)
18. BioGRID ID (e.g., 124439)
19. BindingDB ID (e.g., P00697)
20. ChEMBL ID (e.g., CHEMBL2297)
21. DrugBank ID(e.g., DB06934)
22. GeneID (e.g., 1258585)
23. KEGG ID (e.g., vg:1258585)
24. Ensembl (e.g., ENSMGAT00000011853)
25. GeneTree ID (e.g., ENSGT00940000153832)
26. BRENDA ID (e.g., 3.2.1.17)
27. BioCyc ID (e.g., ARA:AT3G12500-MON)
28. RNAct ID (e.g., P20160)
29. PANTHER ID (e.g., PTHR10206)
30. PROSITE ID (e.g., PS00946)
31. InterPro ID (e.g., IPR018216)
32. EMBL ID (e.g., Y09471)
33. GenBank ID (e.g., BC142014)
34. CCDS ID (e.g., CCDS12044.1)
35. RefSeq ID (e.g., NP_001691.1)
36. UniProt ID (e.g., P19171)
Note: For perform more specific 12 to 36 related search "Advanced Search" facility is recomended.
37. Taxonomy lineage (e.g., Plant)
3. AMPDB Specific Search Facility
This is a specific search facility (the search can also be restricted by clicking on 'Choose a Dataset' option). This search facility returns those entries which are exactly match with the search term. This search facility is case insensitive. Here one can search with followings.
All the same search terms like the "AMPDB Text Search Facility" can also be search here
4. Use AMPDB Target Organism Search Facility
This search facility specifically designed to find one or more target organism of a AMP (the search can also be restricted by clicking on 'Choose a Dataset' option). This search facility is case insensitive. Here one can search in the following way.
By single target organism name
Just type the organism name in the search box (e.g., E.coli or e.coli).
By Multiple target organism name (comma separated or comma space separated)
Type multiple organism name in the search box separated by comma or comma space (e.g., E.coli,S.typhimurium or e.coli, S.typhimurium). One can place as many organism as possible. But this facility will return only those result which contain both target organism.
Note: In some case user may not find the target organism. In that case we suggest to do not write anything on the search box, just click on "Get Organism from Table" option. A table will apprear. The table contain all target organism that we enlisted. You need to find wheather your target organism is enlisted in the table or not. You can search in different way (e.g., Escherichia coli can also write as it is or Escherichia sp. or Escherichia spp. or Escherichia species or E.coli or Escherichia). If your target organism is enlisted in this table then you nedd to write the same way in the "AMPDB Target Organism Search" facility to find the result. Do not bother about case sensitivity.
5. Use AMPDB Protein Physicochemical Properties Search Facility
This is protein physicochemical properties search facility (the search can also be restricted by clicking on 'Choose a Dataset' option). Here One can search by build query by just select the options(s) as need. The user need to click on the "Add Field" to make all fields and options visible.
In all the search field integer of float value expected. A field may be kept blank to build the query. A sample query is atached below in iamge form.
6. Use AMPDB Protein Composition Search Facility
This is Protein Composition search facility (the search can also be restricted by clicking on 'Choose a Dataset' option). Here One can search by build query by just select the options(s) as need.The user need to click on the "Add Field" to make all fields and options visible.
In all the search field integer of float value expected. A field may be kept blank to build the query. A sample query is atached below in iamge form.
7. Use AMPDB Activity Search Facility
In this section various activities are listed, which are found in a AMP. A user can select single or multiple checkbox(s) as per interest. The search can also be restricted by clicking on 'Choose a Dataset' option.
8. Use AMPDB Advanced Search Facility
This is the most advanced search facility of AMPDB, where a user can build the query as he/she wants and search on the database. The search can also be restricted by clicking on 'Choose a Dataset' option. We recommend users to check the demo on advanced search facility of AMPDB on tutorial page. A tutorial demo will add here soon.
9. Understand the Text Format of AMPDB
The text format of AMPDB starts with two-character code followed by 4 blank space characters followed by the data. Each line is kept 80 characters long for better readability of the data. The description of the two-character code is given below.
2 Character Code Description
ID AMPDB Acc/ID
PN Protein Name
PF Protein Family
GN Gene Name
SO Source Organism
PL Protein Length
PE Protein Existence
AC Counts of Amino Acids
AF Frequencies of Amino Acids
MA Missing Amino Acid(s)
MO Most Occurring Amino Acid(s)
LO Less Occurring Amino Acid(s)
BA Hydrophobic Amino Acid(s) Count
LA Hydrophilic Amino Acid(s) Count
AA Acidic Amino Acid(s) Count
BC Basic Amino Acid(s) Count
MC Modified Amino Acid(s) Count
MF Modified Amino Acid(s) Frequencies
MM Molecular Mass
AI Aliphatic Index
II Instability Index (Half Life)
HP Hydrophobicity (GRAVY)
HM Hydrophobic Moment
IP Isoelectric Point
C7 Charge (at pH 7)
SF Secondary Structure Fraction
AR Aromaticity
ME Molar Extinction Coefficient (cysteine|cysteine)
TO Target Organism(s)
AM Antimicrobial Activity
EA Enzymatic Activity
IE Inhibitory Effect
OE Other Biological Activity
XR Database Cross-reference
SQ Sequence
XX Blank Line
// End of an entry



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